samtools/samtools 1.8

on GitHub

• samtools calmd now has a quiet mode. This can be enabled by passing -Q to calmd. (Thanks to Colin Davenport)

• In samtools depth -d 0 will effectively remove the depth limit. (#764)

• Improvements made to samtools collate's interface and documentation. It is now possible to specify an output file name using -o, instead of deriving it from the prefix used for temporary files. The prefix itself is now optional if -o or -O (to stdout) is used. (#780)

• Bug-fixes:

  • Make samtools addreplacerg choose output format by file extension. (#767; reported by Argy Megalios)

  • Merge tests now work on ungzipped data, allowing tests to be run against different deflate libraries.

  • samtools markdup error messages about missing tags have been updated with the suggestion that samtools fixmate is run beforehand. (#765; reported by Yudong Cai)

  • Enables the --reference option for samtools fastq. Now works like other programs when a reference sequence is needed for CRAM files. (#791, reported by Milana Kaljevic)

The samtools-1.8.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.